Protein profile

KP13_00806

RNA polymerase sigma-E factor

Genome: KpKP13

Gene: AHE43171.1 rpoE Structure source: AlphaFold + ColabFold UniProt A0A0H3GTU4
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Amino acids 191
Annotations 7
Features 20
PDB binders 1
Druggability 0.939

Overview

Basic information about this protein and its source genome.

Accession
KP13_00806
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43171.1 rpoE
Status
annotated
Amino acids
191
Structure source
AlphaFold + ColabFold
GO
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place. GO:0006950 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.859
DEG E-value
2.02e-136
Localization
Cytoplasmic
ColabFold pLDDT
82.43

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.939
Structure A0A0H3GTU4
Pocket Pocket 1
P2Rank
Structure A0A0H3GTU4
Pocket No pockets
ColabFold model
FPocket 0.725 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 184 / 4744 genomes with a hit
Normalized 0.039

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:0006950 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
  • GO:0009266 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 189 NCBIfam TIGR02939 RNA polymerase sigma factor RpoE
1 189 InterPro IPR014286 RNA polymerase sigma-70 RpoE type
21 183 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
21 183 InterPro IPR014284 RNA polymerase sigma-70 like domain
1 120 Gene3D G3DSA:1.10.1740.10 -
1 120 FunFam G3DSA:1.10.1740.10:FF:000001 RNA polymerase sigma factor
121 191 FunFam G3DSA:1.10.10.10:FF:000043 RNA polymerase sigma factor
2 104 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
2 104 InterPro IPR013325 RNA polymerase sigma factor, region 2
122 183 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
122 183 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
128 181 CDD cd06171 Sigma70_r4
121 191 Gene3D G3DSA:1.10.10.10 -
121 191 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
25 91 Pfam PF04542 Sigma-70 region 2
25 91 InterPro IPR007627 RNA polymerase sigma-70 region 2
129 180 Pfam PF08281 Sigma-70, region 4
129 180 InterPro IPR013249 RNA polymerase sigma factor 70, region 4 type 2
2 185 PANTHER PTHR43133 RNA POLYMERASE ECF-TYPE SIGMA FACTO
2 185 InterPro IPR039425 RNA polymerase sigma-70 like

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GTU4
AlphaFold — — full sequence — Viewing
ColabFold KP13_00806
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.939
4 0.717
3 0.516

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

51 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
NCA
6IN7
Q06198 122.1 Da LogP 0.18 TPSA 56.0 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.